A relative path template
A relative path template
A relative path template
A relative path template
A relative path template
Title
TOC
Table of contents will be automatically generated by scanning the document for headings.
If you want some headings to be excluded from TOC, you just do:
Following heading will be excluded:
TOC-excluded
This is a very very very very very very very very very long heading
This is a third-level heading
Admonitions
This is a warning class: .warn/.warning
This is an info class: .info
This is an example class: .example
No head
head=false
Tables
Tables with all data
You can insert links into the table by using <ALT: HREF>.
Numbers are rounded to 3 decimals if length > 10.
Tables with subset of data and download available
Tables without data file
```table
caption: Data table
download: true
csvargs:
delimiter: ","
---
ID,Name,Sex,Age
1,Bob,M,49
2,Alice,F,20
```References/Links
- Something needs ref [1]
If links are relative path to local files, they should be relative to the markdown file.
Images
Images are lazy-loaded.
Add a single image
Add images as a combined figure
<!-- no empty lines among the images -->
Relative image path should be relative to the markdown file.
When pyppl_report work as a PyPPL plugin, we usually pass the absolute path. However, when it works as a CLI tool, relative path may be used.
Panels
A set of panels are blocks that only occupy one panel space in the page by using tabs or accordions, based on the number of this set of panels.
Auto-decide to use tabs or accordions
When number of panels <= 4 we will use tabs, otherwise accordions are used.
panel1
panel2
Accordions
panel1
panel2
panel1
panel2
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
panel1
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
panel2
Force tabs or accordions
::: {.panel .accordion head=Panel1}
The quick brown fox jumps over the lazy dog.
:::
::: {.panel head=Panel2}
panel2
:::TOC
Table of contents will be automatically generated by scanning the document for headings.
If you want some headings to be excluded from TOC, you just do:
Following heading will be excluded:
TOC-excluded
This is a very very very very very very very very very long heading
This is a third-level heading
Admonitions
This is a warning class: .warn/.warning
This is an info class: .info
This is an example class: .example
No head
head=false
Tables
Tables with all data
You can insert links into the table by using <ALT: HREF>.
Numbers are rounded to 3 decimals if length > 10.
Tables with subset of data and download available
Tables without data file
```table
caption: Data table
download: true
csvargs:
delimiter: ","
---
ID,Name,Sex,Age
1,Bob,M,49
2,Alice,F,20
```References/Links
- Something needs ref [1]
If links are relative path to local files, they should be relative to the markdown file.
Images
Images are lazy-loaded.
Add a single image
Add images as a combined figure
<!-- no empty lines among the images -->
Relative image path should be relative to the markdown file.
When pyppl_report work as a PyPPL plugin, we usually pass the absolute path. However, when it works as a CLI tool, relative path may be used.
Panels
A set of panels are blocks that only occupy one panel space in the page by using tabs or accordions, based on the number of this set of panels.
Auto-decide to use tabs or accordions
When number of panels <= 4 we will use tabs, otherwise accordions are used.
panel1
panel2
Accordions
panel1
panel2
panel1
panel2
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
panel1
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
panel2
Force tabs or accordions
::: {.panel .accordion head=Panel1}
The quick brown fox jumps over the lazy dog.
:::
::: {.panel head=Panel2}
panel2
:::TOC
Table of contents will be automatically generated by scanning the document for headings.
If you want some headings to be excluded from TOC, you just do:
Following heading will be excluded:
TOC-excluded
This is a very very very very very very very very very long heading
This is a third-level heading
Admonitions
This is a warning class: .warn/.warning
This is an info class: .info
This is an example class: .example
No head
head=false
Tables
Tables with all data
You can insert links into the table by using <ALT: HREF>.
Numbers are rounded to 3 decimals if length > 10.
Tables with subset of data and download available
Tables without data file
```table
caption: Data table
download: true
csvargs:
delimiter: ","
---
ID,Name,Sex,Age
1,Bob,M,49
2,Alice,F,20
```References/Links
- Something needs ref [1]
If links are relative path to local files, they should be relative to the markdown file.
Images
Images are lazy-loaded.
Add a single image
Add images as a combined figure
<!-- no empty lines among the images -->
Relative image path should be relative to the markdown file.
When pyppl_report work as a PyPPL plugin, we usually pass the absolute path. However, when it works as a CLI tool, relative path may be used.
Panels
A set of panels are blocks that only occupy one panel space in the page by using tabs or accordions, based on the number of this set of panels.
Auto-decide to use tabs or accordions
When number of panels <= 4 we will use tabs, otherwise accordions are used.
panel1
panel2
Accordions
panel1
panel2
panel1
panel2
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
panel1
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
The quick brown fox jumps over the lazy dog.
panel2
Force tabs or accordions
::: {.panel .accordion head=Panel1}
The quick brown fox jumps over the lazy dog.
:::
::: {.panel head=Panel2}
panel2
:::pyppl_report
[[Pypi][[2]](#PYPPL-REF-2){.pyppl-report-refindex}][[3]](#PYPPL-REF-3){.pyppl-report-refindex} [[Github][[4]](#PYPPL-REF-4){.pyppl-report-refindex}][[5]](#PYPPL-REF-5){.pyppl-report-refindex} [[PyPPL][[6]](#PYPPL-REF-6){.pyppl-report-refindex}][[7]](#PYPPL-REF-7){.pyppl-report-refindex} [[PythonVers][[8]](#PYPPL-REF-8){.pyppl-report-refindex}][[3]](#PYPPL-REF-3){.pyppl-report-refindex} [[docs][[9]](#PYPPL-REF-9){.pyppl-report-refindex}][[10]](#PYPPL-REF-10){.pyppl-report-refindex} [[Travis building][[11]](#PYPPL-REF-11){.pyppl-report-refindex}][[12]](#PYPPL-REF-12){.pyppl-report-refindex} [[Codacy][[13]](#PYPPL-REF-13){.pyppl-report-refindex}][[14]](#PYPPL-REF-14){.pyppl-report-refindex} [[Codacy coverage][[15]](#PYPPL-REF-15){.pyppl-report-refindex}][[14]](#PYPPL-REF-14){.pyppl-report-refindex}
A report generating system for [PyPPL][[7]](#PYPPL-REF-7){.pyppl-report-refindex}
Installation
Requires pandoc 2.7+ (and wkhtmltopdf 0.12.4+ when creating PDF reports)
pyppl_report requires pandoc/wkhtmltopdf to be installed in $PATH
pip install pyppl_reportUsage
Specifiation of template
pPyClone.config.report_template = """
# {{report.title}}
PyClone[[7]](#PYPPL-REF-7){.pyppl-report-refindex} is a tool using Probabilistic model for inferring clonal population
structure from deep NGS sequencing.
}})
```table
caption: Clusters
file: "{{path.join(job.o.outdir, "tables/cluster.tsv")}}"
rows: 10
```
Nature methods 11.4 (2014): 396.
"""
# or use a template file
pPyClone.config.report_template = "file:/path/to/template.md"Generating report
PyPPL().start(pPyClone).run().report(
'/path/to/report',
title='Clonality analysis using PyClone',
template='bootstrap'
)
# or save report in a directory
PyPPL(name='Awesome-pipeline').start(pPyClone).run().report('/path/to/')
# report generated at ./Awesome-pipeline.report.htmlExtra data for rendering
You can generate a toml file named job.report.data.toml under <job.outdir> with extra data to render the report template. Beyond that, proc attributes and args can also be used.
For example: job.report.data.toml:
description = 'A awesome report for job 1'Then in your template, you can use it:
References
We use [[7]](#PYPPL-REF-7){.pyppl-report-refindex}, [[10]](#PYPPL-REF-10){.pyppl-report-refindex} … to link to the references, so HTML links have to be in-place (in the format of [text](link) instead of [text][link-index]). All references from different processes will be re-ordered and combined.
Built-in themes
Reference
[1]: ref1[2]: https://img.shields.io/pypi/v/pyppl_report?style=flat-square[3]: https://pypi.org/project/pyppl_report/[4]: https://img.shields.io/github/tag/pwwang/pyppl_report?style=flat-square[5]: https://github.com/pwwang/pyppl_report[6]: https://img.shields.io/github/tag/pwwang/pyppl?label=PyPPL&style=flat-square[7]: https://github.com/pwwang/PyPPL[8]: https://img.shields.io/pypi/pyversions/pyppl_report?style=flat-square[9]: https://img.shields.io/readthedocs/pyppl_report.svg?style=flat-square[10]: https://pyppl_report.readthedocs.io/en/latest/[11]: https://img.shields.io/travis/pwwang/pyppl_report?style=flat-square[12]: https://travis-ci.org/pwwang/pyppl_report[13]: https://img.shields.io/codacy/grade/2b7914a18f794248a62d7b36eb2408a3?style=flat-square[14]: https://app.codacy.com/manual/pwwang/pyppl_report/dashboard[15]: https://img.shields.io/codacy/coverage/2b7914a18f794248a62d7b36eb2408a3?style=flat-square